Starting phenix.real_space_refine on Sat Sep 12 16:07:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xyf_33520/09_2026/7xyf_33520.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xyf_33520/09_2026/7xyf_33520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xyf_33520/09_2026/7xyf_33520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xyf_33520/09_2026/7xyf_33520.map" model { file = "/net/cci-nas-00/data/ceres_data/7xyf_33520/09_2026/7xyf_33520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xyf_33520/09_2026/7xyf_33520.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Se 24 7.20 5 P 292 5.49 5 S 25 5.16 5 C 10029 2.51 5 N 3164 2.21 5 O 3787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17321 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 803 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 753 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 3009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3009 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "I" Number of atoms: 2977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2977 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 5281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5281 Classifications: {'peptide': 656} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 631} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 3.72, per 1000 atoms: 0.21 Number of scatterers: 17321 At special positions: 0 Unit cell: (134.16, 140.4, 135.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Se 24 33.99 S 25 16.00 P 292 15.00 O 3787 8.00 N 3164 7.00 C 10029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 553.1 milliseconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2688 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 9 sheets defined 61.9% alpha, 3.3% beta 132 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.590A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.632A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 removed outlier: 4.091A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.515A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.590A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.631A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 removed outlier: 4.092A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS E 110 " --> pdb=" O ASP E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.515A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 129 " --> pdb=" O GLN E 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.624A pdb=" N ARG B 39 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.980A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.806A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.286A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.663A pdb=" N ARG F 39 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.176A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL F 65 " --> pdb=" O PHE F 61 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 removed outlier: 3.745A pdb=" N VAL F 87 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.575A pdb=" N ILE C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.101A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.505A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.559A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.627A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS G 36 " --> pdb=" O ARG G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.155A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.717A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 removed outlier: 3.682A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.954A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.536A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.869A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG D 96 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.891A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 116 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 44 Processing helix chain 'H' and resid 52 through 82 removed outlier: 3.502A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.906A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.805A pdb=" N THR H 112 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS H 117 " --> pdb=" O LYS H 113 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 248 removed outlier: 3.626A pdb=" N GLU K 239 " --> pdb=" O ALA K 235 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU K 242 " --> pdb=" O LYS K 238 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN K 246 " --> pdb=" O LEU K 242 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG K 247 " --> pdb=" O LYS K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 258 removed outlier: 3.706A pdb=" N MSE K 256 " --> pdb=" O ASP K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 260 through 271 removed outlier: 3.736A pdb=" N LYS K 270 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG K 271 " --> pdb=" O MSE K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 281 Processing helix chain 'K' and resid 301 through 340 removed outlier: 3.743A pdb=" N GLU K 312 " --> pdb=" O GLY K 308 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE K 318 " --> pdb=" O MSE K 314 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN K 326 " --> pdb=" O ALA K 322 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU K 330 " --> pdb=" O GLN K 326 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY K 332 " --> pdb=" O GLU K 328 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS K 333 " --> pdb=" O GLN K 329 " (cutoff:3.500A) Processing helix chain 'K' and resid 348 through 352 Processing helix chain 'K' and resid 359 through 366 removed outlier: 3.514A pdb=" N PHE K 365 " --> pdb=" O GLN K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 404 removed outlier: 3.673A pdb=" N ILE K 395 " --> pdb=" O GLN K 391 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASN K 396 " --> pdb=" O ILE K 392 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU K 404 " --> pdb=" O LEU K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 417 through 432 Processing helix chain 'K' and resid 443 through 446 Processing helix chain 'K' and resid 447 through 458 removed outlier: 3.822A pdb=" N LEU K 451 " --> pdb=" O MSE K 447 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA K 455 " --> pdb=" O LEU K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 469 through 482 Processing helix chain 'K' and resid 493 through 500 removed outlier: 3.515A pdb=" N ALA K 497 " --> pdb=" O THR K 493 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA K 498 " --> pdb=" O TYR K 494 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR K 499 " --> pdb=" O ARG K 495 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER K 500 " --> pdb=" O LEU K 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 493 through 500' Processing helix chain 'K' and resid 500 through 509 Processing helix chain 'K' and resid 521 through 525 Processing helix chain 'K' and resid 528 through 537 removed outlier: 3.768A pdb=" N ARG K 532 " --> pdb=" O SER K 528 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE K 537 " --> pdb=" O HIS K 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 565 removed outlier: 3.836A pdb=" N SER K 559 " --> pdb=" O LYS K 555 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE K 563 " --> pdb=" O SER K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 576 through 581 Processing helix chain 'K' and resid 593 through 607 removed outlier: 3.866A pdb=" N MSE K 606 " --> pdb=" O ARG K 602 " (cutoff:3.500A) Processing helix chain 'K' and resid 636 through 644 removed outlier: 3.961A pdb=" N ARG K 642 " --> pdb=" O GLU K 638 " (cutoff:3.500A) Processing helix chain 'K' and resid 645 through 648 Processing helix chain 'K' and resid 670 through 675 Processing helix chain 'K' and resid 678 through 689 removed outlier: 4.317A pdb=" N LEU K 682 " --> pdb=" O ALA K 678 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 695 removed outlier: 3.548A pdb=" N PHE K 695 " --> pdb=" O PRO K 692 " (cutoff:3.500A) Processing helix chain 'K' and resid 702 through 710 removed outlier: 3.646A pdb=" N GLN K 706 " --> pdb=" O ASP K 702 " (cutoff:3.500A) Processing helix chain 'K' and resid 724 through 729 Processing helix chain 'K' and resid 733 through 740 Processing helix chain 'K' and resid 760 through 765 removed outlier: 3.571A pdb=" N LYS K 765 " --> pdb=" O THR K 761 " (cutoff:3.500A) Processing helix chain 'K' and resid 765 through 771 Processing helix chain 'K' and resid 786 through 794 Processing helix chain 'K' and resid 864 through 868 removed outlier: 4.000A pdb=" N ASP K 868 " --> pdb=" O GLN K 865 " (cutoff:3.500A) Processing helix chain 'K' and resid 889 through 894 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.707A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.623A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.955A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.759A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 96 through 97 removed outlier: 6.741A pdb=" N THR F 96 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'K' and resid 407 through 410 removed outlier: 6.719A pdb=" N ASN K 513 " --> pdb=" O ALA K 539 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU K 464 " --> pdb=" O LEU K 491 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 627 through 628 removed outlier: 6.595A pdb=" N THR K 627 " --> pdb=" O VAL K 881 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LYS K 883 " --> pdb=" O THR K 627 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL K 851 " --> pdb=" O TYR K 882 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N VAL K 781 " --> pdb=" O ILE K 852 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE K 832 " --> pdb=" O VAL K 780 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU K 782 " --> pdb=" O PHE K 832 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 519 hydrogen bonds defined for protein. 1512 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 318 hydrogen bonds 580 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 5496 1.36 - 1.52: 8388 1.52 - 1.67: 4257 1.67 - 1.83: 37 1.83 - 1.98: 48 Bond restraints: 18226 Sorted by residual: bond pdb=" C3' DA I 89 " pdb=" O3' DA I 89 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.00e+01 bond pdb=" C3' DG J 101 " pdb=" O3' DG J 101 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.76e+01 bond pdb=" C3' DG J 74 " pdb=" C2' DG J 74 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.49e+01 bond pdb=" C3' DT J 99 " pdb=" O3' DT J 99 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.42e+01 bond pdb=" N7 DA J 113 " pdb=" C5 DA J 113 " ideal model delta sigma weight residual 1.388 1.365 0.023 6.00e-03 2.78e+04 1.41e+01 ... (remaining 18221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 24767 2.30 - 4.61: 994 4.61 - 6.91: 68 6.91 - 9.21: 9 9.21 - 11.52: 5 Bond angle restraints: 25843 Sorted by residual: angle pdb=" O4' DG I 120 " pdb=" C4' DG I 120 " pdb=" C3' DG I 120 " ideal model delta sigma weight residual 106.00 102.70 3.30 6.00e-01 2.78e+00 3.03e+01 angle pdb=" O4' DA J 121 " pdb=" C4' DA J 121 " pdb=" C3' DA J 121 " ideal model delta sigma weight residual 106.00 102.96 3.04 6.00e-01 2.78e+00 2.56e+01 angle pdb=" N PHE K 861 " pdb=" CA PHE K 861 " pdb=" C PHE K 861 " ideal model delta sigma weight residual 114.04 108.01 6.03 1.24e+00 6.50e-01 2.36e+01 angle pdb=" O4' DT J 119 " pdb=" C4' DT J 119 " pdb=" C3' DT J 119 " ideal model delta sigma weight residual 106.00 103.09 2.91 6.00e-01 2.78e+00 2.35e+01 angle pdb=" O4' DC J 104 " pdb=" C4' DC J 104 " pdb=" C3' DC J 104 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 ... (remaining 25838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 8252 30.06 - 60.12: 1934 60.12 - 90.18: 109 90.18 - 120.24: 0 120.24 - 150.31: 3 Dihedral angle restraints: 10298 sinusoidal: 6153 harmonic: 4145 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 dihedral pdb=" CA ALA K 710 " pdb=" C ALA K 710 " pdb=" N ILE K 711 " pdb=" CA ILE K 711 " ideal model delta harmonic sigma weight residual 180.00 156.24 23.76 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA LEU K 737 " pdb=" C LEU K 737 " pdb=" N HIS K 738 " pdb=" CA HIS K 738 " ideal model delta harmonic sigma weight residual 180.00 157.13 22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 10295 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1996 0.053 - 0.105: 743 0.105 - 0.158: 163 0.158 - 0.210: 20 0.210 - 0.263: 4 Chirality restraints: 2926 Sorted by residual: chirality pdb=" CB ILE K 747 " pdb=" CA ILE K 747 " pdb=" CG1 ILE K 747 " pdb=" CG2 ILE K 747 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB THR K 667 " pdb=" CA THR K 667 " pdb=" OG1 THR K 667 " pdb=" CG2 THR K 667 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 2923 not shown) Planarity restraints: 2271 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.063 5.00e-02 4.00e+02 9.53e-02 1.45e+01 pdb=" N PRO G 80 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU K 714 " 0.049 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO K 715 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO K 715 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 715 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " 0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO F 32 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " 0.038 5.00e-02 4.00e+02 ... (remaining 2268 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3010 2.75 - 3.29: 16314 3.29 - 3.83: 35172 3.83 - 4.36: 40263 4.36 - 4.90: 57843 Nonbonded interactions: 152602 Sorted by model distance: nonbonded pdb=" O LEU E 61 " pdb=" NH2 ARG F 36 " model vdw 2.217 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR K 466 " pdb=" OD1 ASP K 503 " model vdw 2.262 3.040 nonbonded pdb=" O2 DC J 46 " pdb=" N1 DG I 101 " model vdw 2.264 2.496 nonbonded pdb=" OG1 THR A 58 " pdb=" O GLN G 104 " model vdw 2.274 3.040 ... (remaining 152597 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.46 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.710 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 18226 Z= 0.697 Angle : 1.013 11.516 25843 Z= 0.751 Chirality : 0.055 0.263 2926 Planarity : 0.007 0.095 2271 Dihedral : 27.107 150.305 7610 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.14 % Allowed : 10.95 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.98 (0.16), residues: 1394 helix: -3.82 (0.10), residues: 783 sheet: -1.65 (0.83), residues: 42 loop : -2.38 (0.21), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 495 TYR 0.014 0.002 TYR K 731 PHE 0.028 0.003 PHE K 832 TRP 0.013 0.003 TRP K 757 HIS 0.015 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00876 / 0.70 (18226) covalent geometry : angle 1.01295 / 0.75 (25843) hydrogen bonds : bond 0.31582 / 20.92 ( 837) hydrogen bonds : angle 10.02553 / 7.13 ( 2092) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 342 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8615 (ttm110) cc_final: 0.8245 (mmm-85) REVERT: A 53 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8353 (tpt-90) REVERT: A 61 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8679 (tp) REVERT: A 115 LYS cc_start: 0.9197 (mttt) cc_final: 0.8992 (mttp) REVERT: A 129 ARG cc_start: 0.8533 (ttt90) cc_final: 0.8279 (tpp80) REVERT: E 48 LEU cc_start: 0.9139 (tp) cc_final: 0.8636 (tp) REVERT: E 53 ARG cc_start: 0.8514 (ttt180) cc_final: 0.8229 (ttm170) REVERT: E 93 GLN cc_start: 0.8800 (tt0) cc_final: 0.8559 (tt0) REVERT: E 126 LEU cc_start: 0.9480 (tp) cc_final: 0.9078 (tt) REVERT: B 53 GLU cc_start: 0.8302 (tp30) cc_final: 0.7973 (tp30) REVERT: B 79 LYS cc_start: 0.8629 (mttp) cc_final: 0.8213 (mmtm) REVERT: F 62 LEU cc_start: 0.9277 (mp) cc_final: 0.9011 (mp) REVERT: F 88 TYR cc_start: 0.8465 (m-10) cc_final: 0.7986 (m-80) REVERT: G 36 LYS cc_start: 0.9215 (mttt) cc_final: 0.8944 (mtpp) REVERT: G 38 ASN cc_start: 0.9019 (m110) cc_final: 0.8799 (m110) REVERT: G 79 ILE cc_start: 0.9490 (tp) cc_final: 0.9122 (tp) REVERT: G 91 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7290 (tm-30) REVERT: G 92 GLU cc_start: 0.7617 (tt0) cc_final: 0.7263 (tt0) REVERT: D 43 LYS cc_start: 0.9334 (mmtt) cc_final: 0.8580 (mtpt) REVERT: D 92 GLN cc_start: 0.8734 (tt0) cc_final: 0.8247 (tm-30) REVERT: D 96 ARG cc_start: 0.8423 (mtt180) cc_final: 0.8186 (ttm110) REVERT: H 56 MET cc_start: 0.8449 (tpp) cc_final: 0.8158 (tpp) REVERT: H 102 GLU cc_start: 0.8279 (tp30) cc_final: 0.7877 (tp30) REVERT: K 256 MSE cc_start: 0.4645 (mtt) cc_final: 0.3925 (mtt) REVERT: K 430 MSE cc_start: 0.5807 (ttm) cc_final: 0.5518 (mtp) REVERT: K 535 MSE cc_start: 0.6099 (mmp) cc_final: 0.5607 (mmm) REVERT: K 544 LEU cc_start: 0.6494 (tp) cc_final: 0.6253 (tp) REVERT: K 712 MSE cc_start: -0.1429 (OUTLIER) cc_final: -0.1691 (mmt) REVERT: K 724 TYR cc_start: 0.7215 (m-80) cc_final: 0.6980 (m-10) REVERT: K 731 TYR cc_start: 0.5015 (m-80) cc_final: 0.4741 (m-80) REVERT: K 732 MSE cc_start: -0.0859 (OUTLIER) cc_final: -0.2050 (mmt) REVERT: K 786 PHE cc_start: 0.6131 (t80) cc_final: 0.5886 (t80) REVERT: K 791 ASP cc_start: 0.6706 (m-30) cc_final: 0.6365 (t70) REVERT: K 797 MSE cc_start: 0.2954 (mmm) cc_final: 0.2418 (mmt) REVERT: K 806 ARG cc_start: 0.5690 (ttt180) cc_final: 0.4651 (ttp-110) REVERT: K 851 VAL cc_start: -0.1058 (OUTLIER) cc_final: -0.1953 (p) REVERT: K 872 ARG cc_start: 0.0772 (mmt180) cc_final: -0.0343 (mpt90) outliers start: 26 outliers final: 8 residues processed: 352 average time/residue: 0.1922 time to fit residues: 93.2105 Evaluate side-chains 243 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 231 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0670 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 5.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS H 44 GLN K 335 GLN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 510 GLN K 772 ASN K 812 GLN K 895 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.101387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.072308 restraints weight = 76687.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.071593 restraints weight = 53153.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.072110 restraints weight = 40773.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072197 restraints weight = 33284.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.072064 restraints weight = 33062.966| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18226 Z= 0.205 Angle : 0.820 9.830 25843 Z= 0.453 Chirality : 0.055 0.404 2926 Planarity : 0.007 0.122 2271 Dihedral : 31.048 143.316 4754 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.19), residues: 1394 helix: -1.93 (0.14), residues: 810 sheet: -1.69 (0.80), residues: 40 loop : -2.03 (0.24), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 779 TYR 0.029 0.002 TYR K 824 PHE 0.026 0.002 PHE K 832 TRP 0.012 0.002 TRP K 397 HIS 0.010 0.002 HIS D 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.20 (18226) covalent geometry : angle 0.81991 / 0.45 (25843) hydrogen bonds : bond 0.10308 / 6.91 ( 837) hydrogen bonds : angle 5.03168 / 3.58 ( 2092) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8699 (ttm110) cc_final: 0.8349 (mmm-85) REVERT: A 53 ARG cc_start: 0.8527 (ttt180) cc_final: 0.8177 (tpt-90) REVERT: A 120 MET cc_start: 0.8627 (mtp) cc_final: 0.8354 (mtp) REVERT: A 129 ARG cc_start: 0.8535 (ttt90) cc_final: 0.8331 (tpp80) REVERT: E 48 LEU cc_start: 0.9226 (tp) cc_final: 0.8736 (tp) REVERT: E 50 GLU cc_start: 0.7742 (mm-30) cc_final: 0.6642 (tp30) REVERT: E 54 TYR cc_start: 0.8880 (m-10) cc_final: 0.8448 (m-10) REVERT: E 76 GLN cc_start: 0.8039 (pm20) cc_final: 0.7748 (pm20) REVERT: E 110 CYS cc_start: 0.8734 (m) cc_final: 0.8015 (m) REVERT: E 126 LEU cc_start: 0.9473 (tp) cc_final: 0.8996 (tt) REVERT: B 43 VAL cc_start: 0.9160 (t) cc_final: 0.8928 (p) REVERT: B 54 THR cc_start: 0.8955 (p) cc_final: 0.8604 (m) REVERT: B 79 LYS cc_start: 0.8445 (mttp) cc_final: 0.8185 (mmtm) REVERT: B 84 MET cc_start: 0.7968 (tpp) cc_final: 0.7618 (tpp) REVERT: B 88 TYR cc_start: 0.8188 (m-10) cc_final: 0.7943 (m-10) REVERT: B 100 PHE cc_start: 0.9083 (m-80) cc_final: 0.8864 (m-80) REVERT: F 63 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7831 (mm-30) REVERT: F 88 TYR cc_start: 0.8416 (m-10) cc_final: 0.7585 (m-80) REVERT: G 36 LYS cc_start: 0.9015 (mttt) cc_final: 0.8795 (mtpp) REVERT: G 84 GLN cc_start: 0.8922 (tp-100) cc_final: 0.8636 (tp-100) REVERT: G 92 GLU cc_start: 0.7828 (tt0) cc_final: 0.7572 (tt0) REVERT: D 43 LYS cc_start: 0.9326 (mmtt) cc_final: 0.8645 (mtmt) REVERT: D 70 ILE cc_start: 0.9443 (mm) cc_final: 0.9224 (mm) REVERT: D 92 GLN cc_start: 0.8549 (tt0) cc_final: 0.8241 (tm-30) REVERT: D 93 THR cc_start: 0.9193 (m) cc_final: 0.8883 (m) REVERT: D 96 ARG cc_start: 0.8295 (mtt180) cc_final: 0.8076 (ttm110) REVERT: H 64 ASN cc_start: 0.8899 (m-40) cc_final: 0.8081 (t0) REVERT: K 245 MSE cc_start: 0.1069 (tpt) cc_final: 0.0572 (tpt) REVERT: K 311 MSE cc_start: 0.5424 (mtp) cc_final: 0.3358 (tmm) REVERT: K 466 TYR cc_start: 0.7057 (t80) cc_final: 0.6567 (t80) REVERT: K 535 MSE cc_start: 0.6249 (mmp) cc_final: 0.5538 (mmm) REVERT: K 582 MSE cc_start: 0.4023 (mtm) cc_final: -0.4280 (ttp) REVERT: K 717 TYR cc_start: 0.7958 (t80) cc_final: 0.7673 (t80) REVERT: K 724 TYR cc_start: 0.7154 (m-10) cc_final: 0.6860 (m-10) REVERT: K 766 LEU cc_start: 0.3790 (mt) cc_final: 0.3546 (tp) REVERT: K 872 ARG cc_start: 0.0428 (mmt180) cc_final: -0.0722 (mpt90) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1672 time to fit residues: 70.6088 Evaluate side-chains 231 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 30.0000 chunk 146 optimal weight: 7.9990 chunk 91 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 129 optimal weight: 0.0270 chunk 62 optimal weight: 3.9990 chunk 64 optimal weight: 0.0770 chunk 70 optimal weight: 0.9980 chunk 80 optimal weight: 30.0000 overall best weight: 1.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS G 19 ASN H 44 GLN H 92 GLN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 739 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.102641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074351 restraints weight = 75747.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.073248 restraints weight = 52760.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.074038 restraints weight = 41847.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074105 restraints weight = 31577.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.073929 restraints weight = 33137.063| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (15 function evaluations) r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 18226 Z= 0.163 Angle : 0.730 10.760 25843 Z= 0.411 Chirality : 0.050 0.428 2926 Planarity : 0.005 0.073 2271 Dihedral : 30.681 141.500 4754 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.08 % Allowed : 4.69 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.20), residues: 1394 helix: -0.90 (0.16), residues: 820 sheet: -1.58 (0.82), residues: 40 loop : -1.70 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 69 TYR 0.018 0.002 TYR K 824 PHE 0.021 0.002 PHE A 78 TRP 0.013 0.002 TRP K 397 HIS 0.007 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (18226) covalent geometry : angle 0.72956 / 0.41 (25843) hydrogen bonds : bond 0.08904 / 6.02 ( 837) hydrogen bonds : angle 4.51562 / 3.22 ( 2092) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 293 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8639 (ttm110) cc_final: 0.8262 (mmm-85) REVERT: A 53 ARG cc_start: 0.8574 (ttt180) cc_final: 0.8371 (tpt-90) REVERT: A 94 GLU cc_start: 0.8020 (tt0) cc_final: 0.7755 (tt0) REVERT: A 120 MET cc_start: 0.8696 (mtp) cc_final: 0.8346 (mtp) REVERT: A 126 LEU cc_start: 0.9324 (tp) cc_final: 0.9086 (tp) REVERT: A 129 ARG cc_start: 0.8538 (ttt90) cc_final: 0.8290 (tpp80) REVERT: E 48 LEU cc_start: 0.9169 (tp) cc_final: 0.8668 (tp) REVERT: E 93 GLN cc_start: 0.8909 (tt0) cc_final: 0.8648 (tm-30) REVERT: E 110 CYS cc_start: 0.8741 (m) cc_final: 0.8157 (m) REVERT: E 118 THR cc_start: 0.9102 (p) cc_final: 0.8839 (t) REVERT: E 126 LEU cc_start: 0.9336 (tp) cc_final: 0.9076 (tt) REVERT: B 43 VAL cc_start: 0.9081 (t) cc_final: 0.8806 (p) REVERT: B 79 LYS cc_start: 0.8378 (mttp) cc_final: 0.8154 (mmtm) REVERT: B 84 MET cc_start: 0.7896 (tpp) cc_final: 0.7673 (tpp) REVERT: B 91 LYS cc_start: 0.8958 (ttmt) cc_final: 0.8671 (tttt) REVERT: B 100 PHE cc_start: 0.9069 (m-80) cc_final: 0.8816 (m-80) REVERT: F 27 GLN cc_start: 0.8896 (mm110) cc_final: 0.8553 (mp10) REVERT: F 63 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7933 (mm-30) REVERT: F 88 TYR cc_start: 0.8450 (m-10) cc_final: 0.7720 (m-80) REVERT: G 36 LYS cc_start: 0.9081 (mttt) cc_final: 0.8766 (mtpp) REVERT: G 38 ASN cc_start: 0.8832 (m110) cc_final: 0.8363 (m110) REVERT: G 84 GLN cc_start: 0.8884 (tp-100) cc_final: 0.8539 (tp-100) REVERT: G 92 GLU cc_start: 0.7708 (tt0) cc_final: 0.7202 (tt0) REVERT: G 102 ILE cc_start: 0.9592 (mm) cc_final: 0.9352 (mm) REVERT: D 43 LYS cc_start: 0.9364 (mmtt) cc_final: 0.8653 (mtmt) REVERT: D 65 ASP cc_start: 0.9057 (OUTLIER) cc_final: 0.8124 (t0) REVERT: D 69 ARG cc_start: 0.8641 (mtt90) cc_final: 0.8227 (mtm-85) REVERT: D 92 GLN cc_start: 0.8580 (tt0) cc_final: 0.8070 (tm-30) REVERT: D 96 ARG cc_start: 0.8237 (mtt180) cc_final: 0.8019 (ttm110) REVERT: H 56 MET cc_start: 0.8419 (tpp) cc_final: 0.8088 (tpp) REVERT: H 64 ASN cc_start: 0.8958 (m-40) cc_final: 0.8061 (t0) REVERT: H 68 GLU cc_start: 0.8160 (tt0) cc_final: 0.7455 (tt0) REVERT: H 92 GLN cc_start: 0.8453 (tm130) cc_final: 0.8149 (tm-30) REVERT: H 102 GLU cc_start: 0.7901 (tp30) cc_final: 0.7229 (tp30) REVERT: K 245 MSE cc_start: 0.0607 (tpt) cc_final: 0.0233 (tpt) REVERT: K 311 MSE cc_start: 0.5555 (mtp) cc_final: 0.4949 (mmm) REVERT: K 323 LEU cc_start: 0.6937 (tp) cc_final: 0.6606 (tp) REVERT: K 535 MSE cc_start: 0.6077 (mmp) cc_final: 0.5557 (mmm) REVERT: K 554 LEU cc_start: 0.3905 (pp) cc_final: 0.3403 (tp) REVERT: K 712 MSE cc_start: 0.6830 (tpp) cc_final: 0.6485 (tpp) REVERT: K 724 TYR cc_start: 0.7114 (m-10) cc_final: 0.6774 (m-10) REVERT: K 850 MSE cc_start: 0.5168 (mmp) cc_final: 0.4623 (tpt) REVERT: K 872 ARG cc_start: 0.0363 (mmt180) cc_final: -0.0857 (mmt90) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.1641 time to fit residues: 69.6241 Evaluate side-chains 227 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 38 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 164 optimal weight: 8.9990 chunk 18 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 85 optimal weight: 50.0000 chunk 102 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN E 93 GLN E 125 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 81 ASN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 716 GLN K 875 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.100123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.072383 restraints weight = 77099.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.071018 restraints weight = 59359.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.071579 restraints weight = 44890.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.071814 restraints weight = 35475.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.071769 restraints weight = 34056.828| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 18226 Z= 0.234 Angle : 0.790 10.117 25843 Z= 0.433 Chirality : 0.050 0.379 2926 Planarity : 0.006 0.079 2271 Dihedral : 30.503 145.545 4754 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.08 % Allowed : 4.53 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.21), residues: 1394 helix: -0.41 (0.17), residues: 809 sheet: -1.16 (0.94), residues: 33 loop : -1.57 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 23 TYR 0.023 0.002 TYR C 57 PHE 0.034 0.002 PHE A 78 TRP 0.012 0.002 TRP K 397 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.23 (18226) covalent geometry : angle 0.79022 / 0.43 (25843) hydrogen bonds : bond 0.08373 / 5.62 ( 837) hydrogen bonds : angle 4.55472 / 3.23 ( 2092) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8130 (tt0) cc_final: 0.7911 (tt0) REVERT: A 120 MET cc_start: 0.8711 (mtp) cc_final: 0.8378 (mtp) REVERT: E 54 TYR cc_start: 0.8971 (m-10) cc_final: 0.8355 (m-10) REVERT: E 79 LYS cc_start: 0.8943 (tmtt) cc_final: 0.8617 (tttp) REVERT: E 80 THR cc_start: 0.8489 (t) cc_final: 0.7789 (t) REVERT: E 126 LEU cc_start: 0.9468 (tp) cc_final: 0.9168 (tt) REVERT: B 79 LYS cc_start: 0.8508 (mttp) cc_final: 0.8242 (mmtm) REVERT: B 84 MET cc_start: 0.7942 (tpp) cc_final: 0.7677 (tpp) REVERT: B 91 LYS cc_start: 0.9021 (ttmt) cc_final: 0.8802 (ttpt) REVERT: F 63 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8134 (mm-30) REVERT: G 36 LYS cc_start: 0.9198 (mttt) cc_final: 0.8839 (mtpp) REVERT: G 38 ASN cc_start: 0.8859 (m110) cc_final: 0.8515 (m110) REVERT: G 102 ILE cc_start: 0.9673 (mm) cc_final: 0.9421 (mm) REVERT: D 38 ILE cc_start: 0.9472 (pt) cc_final: 0.8919 (pt) REVERT: D 43 LYS cc_start: 0.9344 (mmtt) cc_final: 0.8625 (mtpt) REVERT: D 65 ASP cc_start: 0.9054 (t70) cc_final: 0.8356 (t0) REVERT: D 92 GLN cc_start: 0.8743 (tt0) cc_final: 0.8033 (tm-30) REVERT: D 93 THR cc_start: 0.9313 (p) cc_final: 0.8951 (p) REVERT: D 96 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8120 (ttm110) REVERT: H 56 MET cc_start: 0.8364 (tpp) cc_final: 0.8031 (tpp) REVERT: H 64 ASN cc_start: 0.9104 (m-40) cc_final: 0.8221 (t0) REVERT: H 102 GLU cc_start: 0.7963 (tp30) cc_final: 0.7626 (tp30) REVERT: K 311 MSE cc_start: 0.5873 (mtp) cc_final: 0.5303 (mmm) REVERT: K 323 LEU cc_start: 0.7110 (tp) cc_final: 0.6880 (tt) REVERT: K 535 MSE cc_start: 0.6533 (mmp) cc_final: 0.5944 (mmm) REVERT: K 554 LEU cc_start: 0.3513 (pp) cc_final: 0.2921 (tp) REVERT: K 712 MSE cc_start: 0.6507 (tpp) cc_final: 0.6078 (tpp) REVERT: K 815 PHE cc_start: 0.6113 (p90) cc_final: 0.5751 (p90) REVERT: K 850 MSE cc_start: 0.4867 (mmp) cc_final: 0.4384 (tpt) REVERT: K 872 ARG cc_start: 0.0273 (mmt180) cc_final: -0.0438 (mmt90) REVERT: K 875 GLN cc_start: 0.0653 (OUTLIER) cc_final: -0.2739 (mp10) outliers start: 1 outliers final: 0 residues processed: 263 average time/residue: 0.1561 time to fit residues: 60.0730 Evaluate side-chains 207 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 206 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 95 optimal weight: 30.0000 chunk 42 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 142 optimal weight: 0.8980 chunk 99 optimal weight: 30.0000 chunk 41 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 25 ASN C 24 GLN D 44 GLN D 46 HIS D 106 HIS H 44 GLN H 92 GLN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.102545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.073849 restraints weight = 75863.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.072563 restraints weight = 51748.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.073596 restraints weight = 42295.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.073575 restraints weight = 32951.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.073640 restraints weight = 28292.276| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3405 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3405 r_free = 0.3405 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3405 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18226 Z= 0.149 Angle : 0.689 9.759 25843 Z= 0.389 Chirality : 0.048 0.405 2926 Planarity : 0.005 0.069 2271 Dihedral : 30.326 140.352 4754 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1394 helix: 0.00 (0.18), residues: 809 sheet: -1.55 (0.86), residues: 40 loop : -1.41 (0.26), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 39 TYR 0.022 0.002 TYR F 98 PHE 0.032 0.002 PHE K 832 TRP 0.015 0.001 TRP K 397 HIS 0.006 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (18226) covalent geometry : angle 0.68898 / 0.39 (25843) hydrogen bonds : bond 0.07769 / 5.26 ( 837) hydrogen bonds : angle 4.12020 / 2.94 ( 2092) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.9332 (tp) cc_final: 0.9098 (tp) REVERT: A 94 GLU cc_start: 0.8131 (tt0) cc_final: 0.7920 (tt0) REVERT: A 120 MET cc_start: 0.8713 (mtp) cc_final: 0.8251 (mtp) REVERT: E 50 GLU cc_start: 0.7887 (tp30) cc_final: 0.7676 (tp30) REVERT: E 80 THR cc_start: 0.8460 (t) cc_final: 0.7771 (t) REVERT: E 93 GLN cc_start: 0.8813 (tt0) cc_final: 0.8347 (tm-30) REVERT: E 126 LEU cc_start: 0.9383 (tp) cc_final: 0.9160 (tp) REVERT: B 79 LYS cc_start: 0.8529 (mttp) cc_final: 0.8267 (mmtt) REVERT: B 91 LYS cc_start: 0.8876 (ttmt) cc_final: 0.8574 (ttpt) REVERT: F 26 ILE cc_start: 0.9317 (tp) cc_final: 0.9019 (tp) REVERT: F 27 GLN cc_start: 0.8895 (mm110) cc_final: 0.8581 (mp10) REVERT: F 46 ILE cc_start: 0.9176 (mt) cc_final: 0.8928 (mt) REVERT: F 63 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7909 (mm-30) REVERT: F 65 VAL cc_start: 0.9566 (m) cc_final: 0.9324 (p) REVERT: F 88 TYR cc_start: 0.8303 (m-10) cc_final: 0.7580 (m-80) REVERT: F 90 LEU cc_start: 0.9254 (mm) cc_final: 0.8935 (mp) REVERT: F 93 GLN cc_start: 0.7908 (mp10) cc_final: 0.7127 (mp10) REVERT: G 19 ASN cc_start: 0.8637 (m-40) cc_final: 0.8266 (t0) REVERT: G 24 GLN cc_start: 0.8068 (mp10) cc_final: 0.7699 (mp10) REVERT: G 36 LYS cc_start: 0.9090 (mttt) cc_final: 0.8769 (mtpp) REVERT: G 38 ASN cc_start: 0.8781 (m110) cc_final: 0.8508 (m110) REVERT: G 56 GLU cc_start: 0.8571 (mt-10) cc_final: 0.7264 (mt-10) REVERT: G 64 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8396 (tm-30) REVERT: G 83 LEU cc_start: 0.9195 (mm) cc_final: 0.8775 (mm) REVERT: D 43 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8353 (mtpp) REVERT: D 65 ASP cc_start: 0.8725 (t70) cc_final: 0.7426 (t0) REVERT: D 69 ARG cc_start: 0.8518 (mtt90) cc_final: 0.8041 (mtm-85) REVERT: D 92 GLN cc_start: 0.8570 (tt0) cc_final: 0.8162 (tt0) REVERT: D 93 THR cc_start: 0.9227 (p) cc_final: 0.8677 (p) REVERT: H 56 MET cc_start: 0.8345 (tpp) cc_final: 0.8042 (tpp) REVERT: H 64 ASN cc_start: 0.8994 (m-40) cc_final: 0.8152 (t0) REVERT: H 102 GLU cc_start: 0.8094 (tp30) cc_final: 0.7720 (tp30) REVERT: K 256 MSE cc_start: 0.5051 (mtp) cc_final: 0.4210 (mtt) REVERT: K 311 MSE cc_start: 0.5538 (mtp) cc_final: 0.4551 (mmm) REVERT: K 323 LEU cc_start: 0.7022 (tp) cc_final: 0.6725 (tp) REVERT: K 535 MSE cc_start: 0.6538 (mmp) cc_final: 0.5956 (mmm) REVERT: K 554 LEU cc_start: 0.3510 (pp) cc_final: 0.2959 (tp) REVERT: K 712 MSE cc_start: 0.6722 (tpp) cc_final: 0.6454 (tpp) REVERT: K 815 PHE cc_start: 0.6389 (p90) cc_final: 0.6167 (p90) REVERT: K 850 MSE cc_start: 0.5559 (mmp) cc_final: 0.4471 (tpt) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.1518 time to fit residues: 62.9790 Evaluate side-chains 230 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 0.9980 chunk 131 optimal weight: 8.9990 chunk 99 optimal weight: 30.0000 chunk 135 optimal weight: 0.0000 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN F 75 HIS H 44 GLN H 79 HIS H 92 GLN K 510 GLN K 668 ASN K 812 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.103288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.074400 restraints weight = 75712.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.073525 restraints weight = 53200.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.074228 restraints weight = 40133.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.074484 restraints weight = 32293.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.074317 restraints weight = 33260.737| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18226 Z= 0.147 Angle : 0.692 13.229 25843 Z= 0.384 Chirality : 0.047 0.395 2926 Planarity : 0.005 0.065 2271 Dihedral : 30.181 138.232 4754 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.08 % Allowed : 2.30 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.22), residues: 1394 helix: 0.18 (0.18), residues: 815 sheet: -1.34 (0.91), residues: 40 loop : -1.30 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 23 TYR 0.036 0.002 TYR H 37 PHE 0.027 0.001 PHE K 832 TRP 0.016 0.001 TRP K 397 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (18226) covalent geometry : angle 0.69173 / 0.38 (25843) hydrogen bonds : bond 0.07515 / 5.09 ( 837) hydrogen bonds : angle 4.01126 / 2.86 ( 2092) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 275 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8118 (tt0) cc_final: 0.7882 (tt0) REVERT: A 120 MET cc_start: 0.8669 (mtp) cc_final: 0.8169 (mtp) REVERT: E 92 LEU cc_start: 0.9043 (tp) cc_final: 0.8797 (tp) REVERT: E 93 GLN cc_start: 0.8759 (tt0) cc_final: 0.8290 (tm-30) REVERT: E 118 THR cc_start: 0.9162 (p) cc_final: 0.8903 (t) REVERT: B 79 LYS cc_start: 0.8501 (mttp) cc_final: 0.8257 (mmtt) REVERT: B 91 LYS cc_start: 0.8861 (ttmt) cc_final: 0.8576 (ttpt) REVERT: F 26 ILE cc_start: 0.9310 (tp) cc_final: 0.9001 (tp) REVERT: F 27 GLN cc_start: 0.8934 (mm110) cc_final: 0.8512 (mp10) REVERT: F 46 ILE cc_start: 0.9148 (mt) cc_final: 0.8935 (mt) REVERT: F 63 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7639 (mm-30) REVERT: F 90 LEU cc_start: 0.9175 (mm) cc_final: 0.8946 (mp) REVERT: C 56 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7374 (tm-30) REVERT: G 19 ASN cc_start: 0.8563 (m-40) cc_final: 0.8260 (t0) REVERT: G 36 LYS cc_start: 0.9045 (mttt) cc_final: 0.8699 (mtpp) REVERT: G 38 ASN cc_start: 0.8744 (m110) cc_final: 0.8428 (m110) REVERT: G 56 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7331 (mt-10) REVERT: G 91 GLU cc_start: 0.6979 (tm-30) cc_final: 0.5965 (tm-30) REVERT: G 92 GLU cc_start: 0.7588 (tt0) cc_final: 0.7220 (mm-30) REVERT: D 36 ILE cc_start: 0.8685 (pt) cc_final: 0.8078 (mm) REVERT: D 38 ILE cc_start: 0.9621 (pt) cc_final: 0.9119 (tt) REVERT: D 43 LYS cc_start: 0.9270 (mmtt) cc_final: 0.8374 (mtpp) REVERT: D 92 GLN cc_start: 0.8373 (tt0) cc_final: 0.7913 (tm-30) REVERT: D 93 THR cc_start: 0.9143 (p) cc_final: 0.8676 (p) REVERT: D 96 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8254 (ttm110) REVERT: H 56 MET cc_start: 0.8293 (tpp) cc_final: 0.7977 (tpp) REVERT: H 64 ASN cc_start: 0.8957 (m-40) cc_final: 0.8145 (t0) REVERT: H 102 GLU cc_start: 0.7677 (tp30) cc_final: 0.7251 (tp30) REVERT: K 256 MSE cc_start: 0.5117 (mtp) cc_final: 0.4546 (mtt) REVERT: K 311 MSE cc_start: 0.5676 (mtp) cc_final: 0.4875 (mmm) REVERT: K 323 LEU cc_start: 0.6941 (tp) cc_final: 0.6713 (tp) REVERT: K 535 MSE cc_start: 0.6129 (mmp) cc_final: 0.5841 (mmm) REVERT: K 554 LEU cc_start: 0.3264 (pp) cc_final: 0.2764 (tp) REVERT: K 712 MSE cc_start: 0.6756 (tpp) cc_final: 0.6492 (tpp) REVERT: K 815 PHE cc_start: 0.6437 (p90) cc_final: 0.6193 (p90) REVERT: K 850 MSE cc_start: 0.5497 (mmp) cc_final: 0.4422 (tpt) REVERT: K 872 ARG cc_start: 0.0194 (mmm160) cc_final: -0.0986 (mmt-90) outliers start: 1 outliers final: 1 residues processed: 276 average time/residue: 0.1520 time to fit residues: 61.1869 Evaluate side-chains 227 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 56 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 119 optimal weight: 0.1980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.103254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.073510 restraints weight = 75440.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.072880 restraints weight = 50586.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.073814 restraints weight = 38085.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.073838 restraints weight = 27429.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.074090 restraints weight = 25667.053| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 18226 Z= 0.146 Angle : 0.668 12.207 25843 Z= 0.374 Chirality : 0.046 0.385 2926 Planarity : 0.005 0.066 2271 Dihedral : 30.078 138.127 4754 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.22), residues: 1394 helix: 0.36 (0.18), residues: 817 sheet: -1.43 (0.90), residues: 40 loop : -1.16 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 495 TYR 0.016 0.001 TYR K 643 PHE 0.024 0.001 PHE K 726 TRP 0.012 0.001 TRP K 397 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.15 (18226) covalent geometry : angle 0.66795 / 0.37 (25843) hydrogen bonds : bond 0.07367 / 4.99 ( 837) hydrogen bonds : angle 3.92792 / 2.80 ( 2092) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8797 (mtp) cc_final: 0.8276 (mtp) REVERT: E 80 THR cc_start: 0.8839 (p) cc_final: 0.8384 (p) REVERT: E 93 GLN cc_start: 0.8890 (tt0) cc_final: 0.8344 (tm-30) REVERT: E 110 CYS cc_start: 0.8693 (m) cc_final: 0.8128 (m) REVERT: E 118 THR cc_start: 0.9239 (p) cc_final: 0.8993 (t) REVERT: B 79 LYS cc_start: 0.8554 (mttp) cc_final: 0.8235 (mmtt) REVERT: B 91 LYS cc_start: 0.9013 (ttmt) cc_final: 0.8662 (ttpt) REVERT: F 26 ILE cc_start: 0.9343 (tp) cc_final: 0.9021 (tp) REVERT: F 27 GLN cc_start: 0.8997 (mm110) cc_final: 0.8538 (mp10) REVERT: F 46 ILE cc_start: 0.9182 (mt) cc_final: 0.8965 (mt) REVERT: C 56 GLU cc_start: 0.8405 (mt-10) cc_final: 0.7488 (tm-30) REVERT: C 68 ASN cc_start: 0.8446 (m-40) cc_final: 0.8213 (t0) REVERT: G 19 ASN cc_start: 0.8671 (m-40) cc_final: 0.8332 (t0) REVERT: G 36 LYS cc_start: 0.9129 (mttt) cc_final: 0.8722 (mtpp) REVERT: G 38 ASN cc_start: 0.8734 (m110) cc_final: 0.8403 (m110) REVERT: G 91 GLU cc_start: 0.7059 (tm-30) cc_final: 0.6075 (tm-30) REVERT: G 92 GLU cc_start: 0.7766 (tt0) cc_final: 0.7320 (mm-30) REVERT: D 36 ILE cc_start: 0.8672 (pt) cc_final: 0.8170 (mm) REVERT: D 38 ILE cc_start: 0.9659 (pt) cc_final: 0.9277 (tt) REVERT: D 43 LYS cc_start: 0.9329 (mmtt) cc_final: 0.8441 (mtpp) REVERT: D 92 GLN cc_start: 0.8538 (tt0) cc_final: 0.7952 (tm-30) REVERT: D 93 THR cc_start: 0.9154 (p) cc_final: 0.8732 (p) REVERT: D 96 ARG cc_start: 0.8503 (mtm110) cc_final: 0.8241 (ttm110) REVERT: H 64 ASN cc_start: 0.9075 (m-40) cc_final: 0.8266 (t0) REVERT: H 102 GLU cc_start: 0.7935 (tp30) cc_final: 0.7352 (tp30) REVERT: K 256 MSE cc_start: 0.5200 (mtp) cc_final: 0.4702 (mtt) REVERT: K 311 MSE cc_start: 0.5637 (mtp) cc_final: 0.4914 (mmm) REVERT: K 323 LEU cc_start: 0.7042 (tp) cc_final: 0.6713 (tp) REVERT: K 535 MSE cc_start: 0.6196 (mmp) cc_final: 0.5962 (mmm) REVERT: K 712 MSE cc_start: 0.6751 (tpp) cc_final: 0.6358 (tpp) REVERT: K 815 PHE cc_start: 0.6402 (p90) cc_final: 0.6187 (p90) REVERT: K 850 MSE cc_start: 0.5461 (mmp) cc_final: 0.4411 (tpt) REVERT: K 872 ARG cc_start: 0.0253 (mmm160) cc_final: -0.1318 (mmt90) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 0.1505 time to fit residues: 57.9724 Evaluate side-chains 218 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 30.0000 chunk 114 optimal weight: 9.9990 chunk 106 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 85 optimal weight: 40.0000 chunk 18 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 74 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS H 44 GLN H 79 HIS H 92 GLN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.102226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.073765 restraints weight = 76108.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072194 restraints weight = 54416.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.072911 restraints weight = 50216.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.073044 restraints weight = 35675.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.073080 restraints weight = 35248.635| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 18226 Z= 0.173 Angle : 0.685 10.433 25843 Z= 0.382 Chirality : 0.047 0.492 2926 Planarity : 0.005 0.067 2271 Dihedral : 30.040 139.472 4754 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1394 helix: 0.45 (0.18), residues: 815 sheet: -1.57 (0.89), residues: 40 loop : -1.12 (0.27), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 640 TYR 0.026 0.002 TYR H 37 PHE 0.030 0.002 PHE A 78 TRP 0.011 0.001 TRP K 397 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (18226) covalent geometry : angle 0.68497 / 0.38 (25843) hydrogen bonds : bond 0.07266 / 4.90 ( 837) hydrogen bonds : angle 3.99575 / 2.84 ( 2092) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8779 (mtp) cc_final: 0.8285 (mtp) REVERT: E 93 GLN cc_start: 0.8853 (tt0) cc_final: 0.8321 (tm-30) REVERT: E 94 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7840 (tm-30) REVERT: B 79 LYS cc_start: 0.8591 (mttp) cc_final: 0.8255 (mmtt) REVERT: B 91 LYS cc_start: 0.9001 (ttmt) cc_final: 0.8668 (ttpt) REVERT: F 26 ILE cc_start: 0.9345 (tp) cc_final: 0.8957 (tp) REVERT: F 27 GLN cc_start: 0.8984 (mm110) cc_final: 0.8517 (mp10) REVERT: F 46 ILE cc_start: 0.9263 (mt) cc_final: 0.8922 (mt) REVERT: F 63 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7928 (mm-30) REVERT: C 56 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8290 (mt-10) REVERT: G 19 ASN cc_start: 0.8641 (m-40) cc_final: 0.8341 (t0) REVERT: G 36 LYS cc_start: 0.9122 (mttt) cc_final: 0.8741 (mtpp) REVERT: G 38 ASN cc_start: 0.8772 (m110) cc_final: 0.8348 (m110) REVERT: G 83 LEU cc_start: 0.9279 (mm) cc_final: 0.9078 (mm) REVERT: G 91 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6182 (tm-30) REVERT: G 92 GLU cc_start: 0.7846 (tt0) cc_final: 0.7412 (mm-30) REVERT: D 36 ILE cc_start: 0.8743 (pt) cc_final: 0.8188 (mm) REVERT: D 38 ILE cc_start: 0.9703 (pt) cc_final: 0.9309 (tt) REVERT: D 43 LYS cc_start: 0.9309 (mmtt) cc_final: 0.8632 (mtpt) REVERT: D 59 MET cc_start: 0.8819 (mmm) cc_final: 0.7783 (mtt) REVERT: D 92 GLN cc_start: 0.8523 (tt0) cc_final: 0.7917 (tm-30) REVERT: D 93 THR cc_start: 0.9189 (p) cc_final: 0.8832 (p) REVERT: H 64 ASN cc_start: 0.9056 (m-40) cc_final: 0.8276 (t0) REVERT: H 102 GLU cc_start: 0.8036 (tp30) cc_final: 0.7492 (tp30) REVERT: K 256 MSE cc_start: 0.5386 (mtp) cc_final: 0.4910 (mtt) REVERT: K 311 MSE cc_start: 0.5616 (mtp) cc_final: 0.5176 (mmm) REVERT: K 323 LEU cc_start: 0.6999 (tp) cc_final: 0.6650 (tp) REVERT: K 535 MSE cc_start: 0.6169 (mmp) cc_final: 0.5867 (mmm) REVERT: K 712 MSE cc_start: 0.6668 (tpp) cc_final: 0.6286 (tpp) REVERT: K 815 PHE cc_start: 0.6510 (p90) cc_final: 0.6247 (p90) REVERT: K 850 MSE cc_start: 0.5672 (mmp) cc_final: 0.4469 (tpt) REVERT: K 872 ARG cc_start: 0.1242 (mmt180) cc_final: 0.0566 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.1467 time to fit residues: 53.8983 Evaluate side-chains 209 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 146 optimal weight: 30.0000 chunk 150 optimal weight: 0.1980 chunk 154 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 20.0000 chunk 2 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 87 optimal weight: 30.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 110 ASN H 44 GLN H 92 GLN ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.101463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.073427 restraints weight = 75794.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.072352 restraints weight = 57818.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.072475 restraints weight = 44229.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072847 restraints weight = 37956.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.072785 restraints weight = 34353.000| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18226 Z= 0.192 Angle : 0.705 9.865 25843 Z= 0.391 Chirality : 0.047 0.362 2926 Planarity : 0.005 0.063 2271 Dihedral : 30.042 140.333 4754 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.08 % Allowed : 0.82 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.22), residues: 1394 helix: 0.44 (0.18), residues: 813 sheet: -1.64 (0.89), residues: 40 loop : -1.14 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 602 TYR 0.020 0.002 TYR E 54 PHE 0.033 0.002 PHE A 78 TRP 0.013 0.001 TRP K 397 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.19 (18226) covalent geometry : angle 0.70469 / 0.39 (25843) hydrogen bonds : bond 0.07310 / 4.92 ( 837) hydrogen bonds : angle 4.07773 / 2.90 ( 2092) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 242 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8814 (mtp) cc_final: 0.8378 (mtp) REVERT: E 93 GLN cc_start: 0.8722 (tt0) cc_final: 0.8369 (tm-30) REVERT: E 94 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7570 (tm-30) REVERT: B 79 LYS cc_start: 0.8535 (mttp) cc_final: 0.8260 (mmtt) REVERT: B 91 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8807 (ttpt) REVERT: F 26 ILE cc_start: 0.9305 (tp) cc_final: 0.8959 (tp) REVERT: F 27 GLN cc_start: 0.8914 (mm110) cc_final: 0.8493 (mp10) REVERT: F 46 ILE cc_start: 0.9222 (mt) cc_final: 0.8961 (mt) REVERT: F 63 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7898 (mm-30) REVERT: G 19 ASN cc_start: 0.8531 (m-40) cc_final: 0.8260 (t0) REVERT: G 36 LYS cc_start: 0.9077 (mttt) cc_final: 0.8727 (mtpp) REVERT: G 38 ASN cc_start: 0.8739 (m110) cc_final: 0.8321 (m110) REVERT: G 91 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6129 (tm-30) REVERT: G 92 GLU cc_start: 0.7829 (tt0) cc_final: 0.7492 (mm-30) REVERT: D 36 ILE cc_start: 0.8712 (pt) cc_final: 0.8085 (mm) REVERT: D 38 ILE cc_start: 0.9694 (pt) cc_final: 0.9308 (tt) REVERT: D 43 LYS cc_start: 0.9288 (mmtt) cc_final: 0.8651 (mtpt) REVERT: D 92 GLN cc_start: 0.8520 (tt0) cc_final: 0.8014 (tm-30) REVERT: D 93 THR cc_start: 0.9193 (p) cc_final: 0.8725 (p) REVERT: H 56 MET cc_start: 0.8296 (tpp) cc_final: 0.8042 (tpp) REVERT: H 64 ASN cc_start: 0.9058 (m-40) cc_final: 0.8359 (t0) REVERT: H 102 GLU cc_start: 0.8051 (tp30) cc_final: 0.7487 (tp30) REVERT: K 256 MSE cc_start: 0.4968 (mtp) cc_final: 0.4511 (mtt) REVERT: K 311 MSE cc_start: 0.5776 (mtp) cc_final: 0.5358 (mmm) REVERT: K 323 LEU cc_start: 0.7056 (tp) cc_final: 0.6714 (tp) REVERT: K 535 MSE cc_start: 0.6272 (mmp) cc_final: 0.5942 (mmm) REVERT: K 712 MSE cc_start: 0.6557 (tpp) cc_final: 0.5919 (tpp) REVERT: K 850 MSE cc_start: 0.5150 (mmp) cc_final: 0.4127 (tpt) REVERT: K 872 ARG cc_start: 0.1369 (mmt180) cc_final: 0.0696 (mmt-90) outliers start: 1 outliers final: 0 residues processed: 243 average time/residue: 0.1415 time to fit residues: 51.5870 Evaluate side-chains 211 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 145 optimal weight: 5.9990 chunk 44 optimal weight: 0.2980 chunk 72 optimal weight: 40.0000 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 96 optimal weight: 20.0000 chunk 74 optimal weight: 30.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 79 HIS H 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.103242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.074813 restraints weight = 75775.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.073576 restraints weight = 53932.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.074452 restraints weight = 43092.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.074568 restraints weight = 32583.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.074576 restraints weight = 29762.713| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18226 Z= 0.141 Angle : 0.674 8.144 25843 Z= 0.375 Chirality : 0.046 0.385 2926 Planarity : 0.005 0.068 2271 Dihedral : 29.945 136.609 4754 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.23), residues: 1394 helix: 0.57 (0.18), residues: 817 sheet: -1.71 (0.89), residues: 40 loop : -0.99 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 305 TYR 0.022 0.001 TYR H 37 PHE 0.020 0.001 PHE A 78 TRP 0.017 0.002 TRP K 397 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (18226) covalent geometry : angle 0.67358 / 0.38 (25843) hydrogen bonds : bond 0.07188 / 4.87 ( 837) hydrogen bonds : angle 3.83921 / 2.75 ( 2092) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8750 (mtp) cc_final: 0.8235 (mtp) REVERT: E 92 LEU cc_start: 0.9136 (tp) cc_final: 0.8887 (tp) REVERT: E 93 GLN cc_start: 0.8810 (tt0) cc_final: 0.8424 (tm-30) REVERT: E 94 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7648 (tm-30) REVERT: E 118 THR cc_start: 0.9189 (p) cc_final: 0.8959 (t) REVERT: E 120 MET cc_start: 0.8985 (mmm) cc_final: 0.8695 (mmp) REVERT: B 79 LYS cc_start: 0.8492 (mttp) cc_final: 0.8183 (mmtt) REVERT: B 91 LYS cc_start: 0.8911 (ttmt) cc_final: 0.8558 (ttpt) REVERT: F 26 ILE cc_start: 0.9316 (tp) cc_final: 0.9021 (tp) REVERT: F 27 GLN cc_start: 0.8954 (mm110) cc_final: 0.8562 (mp10) REVERT: F 46 ILE cc_start: 0.9171 (mt) cc_final: 0.8923 (mt) REVERT: F 63 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7763 (mm-30) REVERT: C 56 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7650 (tm-30) REVERT: G 19 ASN cc_start: 0.8572 (m-40) cc_final: 0.8302 (t0) REVERT: G 36 LYS cc_start: 0.9139 (mttt) cc_final: 0.8854 (mmmt) REVERT: G 38 ASN cc_start: 0.8666 (m110) cc_final: 0.8266 (m110) REVERT: G 83 LEU cc_start: 0.9263 (mm) cc_final: 0.9055 (mm) REVERT: G 91 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6162 (tm-30) REVERT: G 92 GLU cc_start: 0.7717 (tt0) cc_final: 0.6884 (mm-30) REVERT: D 36 ILE cc_start: 0.8667 (pt) cc_final: 0.8102 (mm) REVERT: D 43 LYS cc_start: 0.9294 (mmtt) cc_final: 0.8662 (mtpt) REVERT: D 59 MET cc_start: 0.8625 (mmm) cc_final: 0.8153 (mtt) REVERT: D 92 GLN cc_start: 0.8521 (tt0) cc_final: 0.7987 (tm-30) REVERT: D 93 THR cc_start: 0.9131 (p) cc_final: 0.8767 (p) REVERT: H 42 LEU cc_start: 0.9357 (tt) cc_final: 0.9007 (tt) REVERT: H 64 ASN cc_start: 0.9077 (m-40) cc_final: 0.8351 (t0) REVERT: K 256 MSE cc_start: 0.5239 (mtp) cc_final: 0.4726 (mtt) REVERT: K 267 MSE cc_start: 0.3895 (tmm) cc_final: 0.3386 (tmm) REVERT: K 283 LYS cc_start: 0.2463 (pttm) cc_final: 0.2070 (tptm) REVERT: K 311 MSE cc_start: 0.5764 (mtp) cc_final: 0.5369 (mmm) REVERT: K 323 LEU cc_start: 0.7088 (tp) cc_final: 0.6865 (tp) REVERT: K 535 MSE cc_start: 0.6464 (mmp) cc_final: 0.6177 (mmm) REVERT: K 606 MSE cc_start: 0.6039 (ptp) cc_final: 0.5712 (ptp) REVERT: K 607 MSE cc_start: 0.1047 (mmt) cc_final: 0.0796 (mmt) REVERT: K 712 MSE cc_start: 0.6553 (tpp) cc_final: 0.6127 (tpp) REVERT: K 850 MSE cc_start: 0.5257 (mmp) cc_final: 0.4197 (tpt) REVERT: K 872 ARG cc_start: 0.1166 (mmt180) cc_final: 0.0342 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.1456 time to fit residues: 55.6900 Evaluate side-chains 217 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 chunk 34 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 115 optimal weight: 30.0000 chunk 116 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 83 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 125 GLN F 93 GLN G 73 ASN G 110 ASN H 44 GLN ** H 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.100359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.071882 restraints weight = 76937.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.071036 restraints weight = 56297.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.071333 restraints weight = 48533.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071435 restraints weight = 38089.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.071500 restraints weight = 37187.320| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 18226 Z= 0.253 Angle : 0.788 9.582 25843 Z= 0.431 Chirality : 0.049 0.334 2926 Planarity : 0.006 0.069 2271 Dihedral : 30.011 141.379 4754 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.08 % Allowed : 0.58 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.22), residues: 1394 helix: 0.33 (0.18), residues: 813 sheet: -1.33 (0.99), residues: 33 loop : -1.14 (0.27), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 305 TYR 0.026 0.002 TYR K 824 PHE 0.045 0.002 PHE A 78 TRP 0.011 0.002 TRP K 397 HIS 0.010 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.25 (18226) covalent geometry : angle 0.78753 / 0.43 (25843) hydrogen bonds : bond 0.07702 / 5.15 ( 837) hydrogen bonds : angle 4.36660 / 3.13 ( 2092) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3154.50 seconds wall clock time: 55 minutes 13.95 seconds (3313.95 seconds total)